Contacts of the strand formed by residues 26 - 35 (chain C) in PDB entry 3RT0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 26 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C SER* 1.3 79.1 + - - +
27C CYS* 1.3 61.7 + - - +
115C ASN* 3.3 28.3 - - - +
140C VAL* 3.5 21.6 - - + +
141C VAL* 3.0 12.4 - - - +
142C ASP* 2.3 36.9 + - - +
143C VAL* 4.1 3.8 - - - +
149C LYS* 3.8 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLN* 1.3 74.8 - - - +
28C SER* 1.3 64.9 + - - +
139C PHE* 4.5 2.1 - - - -
140C VAL* 3.5 2.5 - - - +
141C VAL* 2.8 40.8 + - - +
143C VAL* 3.9 8.7 - - + +
149C LYS* 3.6 34.3 - - + +
152C THR* 3.4 37.7 - - - -
153C CYS* 3.6 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C CYS* 1.3 78.6 - - - +
29C SER* 1.3 67.6 + - - +
30C THR* 5.6 0.2 + - - -
138C SER* 5.6 1.4 - - - -
139C PHE* 2.8 25.3 + - - -
140C VAL* 3.5 16.6 - - - +
149C LYS* 4.5 6.9 - - - +
153C CYS* 4.0 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C SER* 1.3 79.8 + - - +
30C THR* 1.3 75.9 + - - +
138C SER* 3.3 2.9 - - - -
139C PHE* 3.2 50.7 + - - +
153C CYS* 4.1 4.5 - - - -
157C GLU* 2.8 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C SER* 1.3 85.0 + - - +
31C LEU* 1.3 75.4 + - - +
32C VAL* 4.9 4.9 - - + -
136C ILE* 3.9 22.7 - - + -
137C GLU 3.5 11.0 - - - +
138C SER* 3.5 11.8 - - - -
157C GLU* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C THR* 1.3 83.1 - - - +
32C VAL* 1.3 66.9 - - - +
135C ALA 3.9 0.2 - - - +
136C ILE* 3.4 4.5 - - - +
137C GLU 2.7 40.0 + - - +
139C PHE* 4.5 2.7 - - + -
157C GLU* 3.6 52.9 - - + +
160C ILE* 3.8 26.5 - - + -
161C GLN* 3.7 32.1 - - + +
164C LEU* 4.0 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C THR* 4.9 4.9 - - + -
31C LEU* 1.3 81.2 - - - +
33C LYS* 1.3 70.2 + - - +
34C HIS 4.9 0.4 - - - +
134C LEU* 3.2 28.5 - - + -
135C ALA 3.3 4.5 - - - -
136C ILE* 3.6 25.8 - - + -
161C GLN* 4.6 9.7 + - - +
164C LEU* 4.4 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C VAL* 1.3 80.7 - - - +
34C HIS* 1.3 74.0 + - - +
35C ILE* 3.8 8.7 + - + +
133C THR 3.8 0.2 - - - +
134C LEU* 3.4 4.9 - - - +
135C ALA* 2.8 39.8 + - + +
161C GLN* 4.3 8.2 - - - +
164C LEU* 3.9 32.1 - - + +
165C ASN* 3.2 30.7 + - - +
168C ALA* 3.7 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C VAL* 4.9 0.6 - - - +
33C LYS* 1.3 89.9 - - - +
35C ILE* 1.3 79.5 + - - +
36C LYS* 4.2 25.1 + - + +
125C GLU* 2.9 53.1 + - - +
127C ILE* 3.6 31.1 + - + +
130C LYS 4.9 3.4 + - - -
132C GLY* 4.1 3.8 + - - -
133C THR 3.5 10.5 + - - -
134C LEU* 4.1 5.0 - - + +
172C GLU* 4.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LYS* 4.1 8.5 - - + +
34C HIS* 1.3 82.5 + - - +
36C LYS* 1.3 61.8 + - - +
37C ALA* 2.9 16.0 + - + +
42C VAL* 4.0 21.1 - - + -
132C GLY* 3.4 1.9 - - - -
133C THR* 2.7 36.2 + - - +
135C ALA* 3.9 26.9 - - + -
164C LEU* 5.0 0.4 - - + +
167C LEU* 3.9 27.1 - - + -
168C ALA* 3.6 22.2 - - + +
171C THR* 3.1 29.4 - - - +
172C GLU* 3.7 5.2 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il